Chair: J. B. Flanegan. Graduate Coordinator: C. M. Allen. IDP Advanced Concentration Director: M.S. Kilberg. Distinguished Professor: B. M. Dunn. Professors: C. M. Allen, Jr.; B. D. Cain; P. W. Chun; J. B. Flanegan; S.C. Frost; M. S. Kilberg; P. J. Laipis; T. W. O'Brien; D. L. Purich; S. M. Schuster; T. P. Yang. Scientist: N. D. Denslow. Associate Professors: R. J. Cohen; T. H. Mareci; P. M. McGuire. Associate Scientists: R. D. Allison; M. J. Koroly. Assistant Professors: M. Agbandje-McKenna; L. B. Bloom; J. Bungert; A. S. Edison; R. McKenna.
The Department of Biochemistry and Molecular Biology faulty mentor Ph.D. students in the College of Medicine interdisciplinary program (IDP) in medical sciences. Students who are interested in pursuing a doctoral degree can view specific features of the biochemistry and molecular biology concentration at http://www.med.ufl.edu.biochem and http://idp.med.ufl.edu/. Admission information is found on the IDP site.
Department faculty also mentor Ph.D. students in other college programs and participate actively in the research and teaching functions of various centers such as the Center for Mammalian Genetics and the Center for Structural Biology. The Department offers a wide variety of courses for graduate students studying in the life sciences.
The research expertise of the faculty spans the areas from cell biology, metabolism, and molecular biology to physical biochemistry/structural biology. Current research interests include viral protease inhibitors, viral RNA replication, bioenergetics and proton translocation, X-chromosome structure and function, cytoskeletal assembly and dynamics, enzyme mechanism and control, chromatin structure, gene expression and regulation, mitochondrial biogenesis and evolution, genetics of inherited disease, nutrient membrane transporters, protein site-directed mutagenesis, ribosome structure and function, signal transduction,, structural biology of macromolecules, protein-nucleic acid interactions, transgenic animal models, and virus crystal structure.
Prospective graduate students should have adequate training in chemistry and biology. Minor deficiencies may be made up immediately after entering graduate school. Previous undergraduate experience in a research laboratory is highly recommended. Doctoral students are required to take a core IDP course in the fall of their first year and beginning in the spring semester students take advanced classes in areas of interest. Specific advanced level courses may be recommended by the student's supervisory chair and committee.
The following courses are open to all graduate students and advanced undergraduates. Additional courses are listed in the Advanced Concentration in Biochemistry and Molecular Biology section under Medical Sciences.
BCH 5026—Biochemistry and Molecular Biology for Pharmacy Students (4) Prereq: CHM 2211, 3217, or equivalents or consent of instructor. Introduction to physical biochemistry, intermediary metabolism, and molecular biology. Surveys of structure, functional properties, synthesis and degradation of amino acid, proteins, carbohydrates, lipids and nucleic acids. Clinical biochemistry topics of interest to pharmacy students.
BCH 5413—Mammalian Molecular Biology and Genetics (3) Prereq: BCH 3025, 4014, CHM 3218, 4207, MCB 4303, or PCB 3063 or consent of instructor. Biochemical and genetic approaches to understanding vertebrate and particularly mammalian molecular biology, moving from basic processes of replication, transcription, and protein synthesis to signal transduction, cell cycle, cancer, genomics, and developmental genetics.
BCH 6156C—Research Methods in Biochemistry (1-4; max: 8) Prereq: Coreq: BCH 6415, 6740. Only by special arrangement. Biochemical research in which the student refines research techniques in physical biochemistry, intermediary metabolism, molecular biology, and cell biology under supervision of faculty member.
BCH 6206—Advanced Metabolism (3) Prereq: BCH 4024, CHM 4207, or consent of instructor. One of three core biochemistry courses. Reactions of intermediary metabolism with emphasis on their integrations, mechanisms, and control. Extensive examples from current literature.
BCH 6207—Advanced Metabolism: Role of Membranes in Signal Transduction and Metabolic Control (1) Prereq: BCH 3025, 4024, CHM 3218, 4207, GMS 6001, or consent of instructor. Fundamentals of membrane biochemistry. Discussions of membrane structure, nutrient and ion transport, protein targeting, and signal transduction. Experimental methods and techniques used to gather and analyze data related to membrane biochemistry and its regulation.
BCH 6208—Advanced Metabolism: Regulation of Key Reactions in Carbohydrate and Lipid Metabolism (1) Prereq: BCH 3025, 4024, CHM 3218, 4207, GMS 6001, or consent of instructor. Key reactions in metabolic pathways of carbohydrate and lipid metabolism with special attention to exploration of experimental basis for current understanding of these processes. Understanding of interactions between major metabolic pathways and control of pathways under different physiological conditions.
BCH 6209—Advanced Metabolism: Regulation of Key Reactions in Amino Acid and Nucleotide Metabolism (1) Prereq: BCH 3025, 4024, CHM 3218, 4207, GMS 6001, or consent of instructor. Special attention to understanding interactions between major metabolic pathways and control of these pathways under different physiological conditions. Structural basis of enzyme function and regulation.
BCH 6296—Advanced Topics in Metabolic Control (1; max: 6) Prereq: Coreq: BCH 6206 or consent of instructor; see course description under Medical Sciences––Biochemistry and Molecular Biology. Thermodynamic, allosteric, hormonal, and genetic control of metabolic reactions.
BCH 6415—Advanced Molecular and Cell Biology (3) Prereq: BCH 4024, CHM 4207, MCB 4303, or consent of instructor. PCB 3063 or a similar course in genetics recommended. One of three core biochemistry courses. Molecular biology of pro- and eukaryotic organisms, emphasis on understanding experimental approaches which led to recent developments. Chromosome structure and organization, advances in recombinant DNA technology, DNA replication, RNA transcription and protein synthesis, and selected aspects of molecular regulation of gene expression.
BCH 6740—Physical Biochemistry/Structural Biology (3) Prereq: BCH 4024, CHM 4207, or consent of instructor. Course in physical chemistry recommended. One of three core biochemistry courses. Physical chemistry of biological molecules and techniques to study their properties. Approaches to structure determination.
BCH 6741C—Magnetic Resonance Imaging and Spectroscopy in Living Systems (1-2; max: 2) Prereq: BCH 6740 or equivalent or consent of instructor. MR imaging methods used to study structure of cells, tissues, and whole animals. MR spectroscopy methods for monitoring biochemistry in living animals . Sample preparation, operation of instrumentation, and data analysis.
BCH 6743—Biochemical Energetics (1) Prereq: BCH 3025, CHM 3216, 4207, or consent of instructor. Molecular and structural interpretation of energy transformation in biological systems including protein-protein interaction, protein self-assembly, and protein-nucleic acid interaction. S/U.
BCH 6744C—Molecular Structure Determination by X-ray Crystallography (1-2; max: 2) Prereq: BCH 6740 or equivalent or consent of instructor. Detailed theoretical and practical instruction on technique of x-ray crystallography utilized for three-dimensional structure determination of macromolecules in studies aimed at structure-function elucidation.
BCH 6745C—Molecular Structure and Dynamics of NMR Spectroscopy (1-2; max: 2) Prereq: BCH 6740 or equivalent or consent of instructor. Theoretical and practical introduction to macromolecular NMR spectroscopy. Basics of multidimensional NMR for structure and dynamics measurements. Hands-on training in modern NMR.
BCH 6746—Structural Biology: Macromolecular Structure Determination (1; max: 3) Prereq: BCH 3025, 4024, CHM 3218, 4207, GMS 6001 or consent of instructor. Experimental approaches to biological machromolecular structure determination. Emphasis on current understanding or protein-protein, protein-nucleic acid structure motifs.
BCH 6747—Structural Biology/Advanced Physical Biochemistry: Spectroscopy and Hydrodynamics (1) Prereq: BCH 3025, 4024, CHM 3218, 4207, GMS 6001, or consent of instructor. Application of spectroscopic techniques (circular dichroism, fluorescence, nuclear magnetic resonance) to determine the structure of biological macromolecules. Hydrodynamic approaches including light scattering, molecular diffusion, viscosity, and ultracentrifugation.
BCH 6749C—Numerical Methods in Structural Biology (1) Prereq: BCH 6740 or equivalent or constent of instructor. Introduction to mathematical and computational methods needed to understand current structural models, biophysical processes, data acquisition methods, and analysis of data acquired with current techniques.
BCH 6876—Recent Advances in Membrane Biology (1) Prereq: general biochemistry or consent of instructor. Literature presented by students and faculty, discussed in depth. Emphasis on current developments, data, interpretation, and critical analysis. S/U.
BCH 6877—Recent Advances in Structural Biology (1; max: 8) Prereq: general biochemistry or consent of instructor. Literature on structural biology presented by students and faculty, discussed in depth. Current developments, data interpretation, and critical analysis. S/U.
BCH 6878—Recent Advances in Cytoskeletal Processes (1; max: 8) Prereq: general biochemistry or consent of instructor. Literature on cytoskeletal processes presented by students and faculty, discussed in depth. Current developments, data interpretation, and critical analysis. S/U.
BCH 6910—Supervised Research (1-5; max: 5) S/U.
BCH 6936—Biochemistry Seminar (1; max: 20) Prereq: Required of graduate students in biochemistry; open to other by special arrangment. Research reports and discussions of current research literature given by graduate students, departmental faculty, and invited speakers.
BCH 6940—Supervised Teaching (1-5; max: 5) S/U.
BCH 6971—Research for Master's Thesis (1-15) S/U.
BCH 7410—Advanced Gene Regulation (1; max: 3) Prereq: GMS 6001 or consent of instructor. Literature-based assessment of most recent advances in factors governing eukaryotic gene regulation.
BCH 7515—Structural Biology/Advanced Physical Biochemistry: Kinetics and Thermodynamics (1) Prereq: BCH 4024, CHM 3218, 4207, GMS 6001, or consent of instructor. Fundamentals of chemical kinetics and thermodynamic analysis of equilibria. Emphasis on application of this knowledge to understanding basic enzyme kinetics, pulse-chase kinetics, protein polymerization, DNA dynamics, protein-nucleic acid interactions, and cooperative ligand binding.
BCH 7979—Advanced Research (1-12) Research for doctoral students before admission to candidacy. Designed for students with a master's degree in the field of study or for students who have been accepted for a doctoral program. Not open to students who have been admitted to candidacy. S/U.
BCH 7980—Research for Doctoral Dissertation (1-15) S/U.
GMS 6195—Chromatin Structure and Gene Expression Journal Colloquy (1; max: 12) Prereq: consent of instructor. Critical presentations and discussions of recent original articles in literature. S/U.